Targeting non-structural proteins of Hepatitis C virus for predicting repurposed drugs using QSAR and machine learning approaches.

Hepatitis C virus (HCV) infection causes viral hepatitis leading to hepatocellular carcinoma. Despite the clinical use of direct-acting antivirals (DAAs) still there is treatment failure in 5-10% cases. Therefore, it is crucial to develop new antivirals against HCV. In this endeavor, we developed the "Anti-HCV" platform using machine learning and quantitative structure-activity relationship (QSAR) approaches to predict repurposed drugs targeting HCV non-structural (NS) proteins. We retrieved experimentally validated small molecules from the ChEMBL database with bioactivity (IC50/EC50) against HCV NS3 (454), NS3/4A (495), NS5A (494) and NS5B (1671) proteins. These unique compounds were divided into training/testing and independent validation datasets. Relevant molecular descriptors and fingerprints were selected using a recursive feature elimination algorithm. Different machine learning techniques viz. support vector machine, k-nearest neighbour, artificial neural network, and random forest were used to develop the predictive models. We achieved Pearson's correlation coefficients from 0.80 to 0.92 during 10-fold cross validation and similar performance on independent datasets using the best developed models. The robustness and reliability of developed predictive models were also supported by applicability domain, chemical diversity and decoy datasets analyses. The "Anti-HCV" predictive models were used to identify potential repurposing drugs. Representative candidates were further validated by molecular docking which displayed high binding affinities. Hence, this study identified promising repurposed drugs viz. naftifine, butalbital (NS3), vinorelbine, epicriptine (NS3/4A), pipecuronium, trimethaphan (NS5A), olodaterol and vemurafenib (NS5B) etc. targeting HCV NS proteins. These potential repurposed drugs may prove useful in antiviral drug development against HCV.

Hepatitis C Virus Infection Is Inhibited by a Noncanonical Antiviral Signaling Pathway Targeted by NS3-NS4A.

The hepatitis C virus (HCV) NS3-NS4A protease complex is required for viral replication and is the major viral innate immune evasion factor. NS3-NS4A evades antiviral innate immunity by inactivating several proteins, including MAVS, the signaling adaptor for RIG-I and MDA5, and Riplet, an E3 ubiquitin ligase that activates RIG-I. Here, we identified a Tyr-16-Phe (Y16F) change in the NS4A transmembrane domain that prevents NS3-NS4A targeting of Riplet but not MAVS. This Y16F substitution reduces HCV replication in Huh7 cells, but not in Huh-7.5 cells, known to lack RIG-I signaling. Surprisingly, deletion of RIG-I in Huh7 cells did not restore Y16F viral replication. Rather, we found that Huh-7.5 cells lack Riplet expression and that the addition of Riplet to these cells reduced HCV Y16F replication, whereas the addition of Riplet lacking the RING domain restored HCV Y16F replication. In addition, TBK1 inhibition or IRF3 deletion in Huh7 cells was sufficient to restore HCV Y16F replication, and the Y16F protease lacked the ability to prevent IRF3 activation or interferon induction. Taken together, these data reveal that the NS4A Y16 residue regulates a noncanonical Riplet-TBK1-IRF3-dependent, but RIG-I-MAVS-independent, signaling pathway that limits HCV infection.IMPORTANCE The HCV NS3-NS4A protease complex facilitates viral replication by cleaving and inactivating the antiviral innate immune signaling proteins MAVS and Riplet, which are essential for RIG-I activation. NS3-NS4A therefore prevents IRF3 activation and interferon induction during HCV infection. Here, we uncover an amino acid residue within the NS4A transmembrane domain that is essential for inactivation of Riplet but does not affect MAVS cleavage by NS3-NS4A. Our study reveals that Riplet is involved in a RIG-I- and MAVS-independent signaling pathway that activates IRF3 and that this pathway is normally inactivated by NS3-NS4A during HCV infection. Our study selectively uncouples these distinct regulatory mechanisms within NS3-NS4A and defines a new role for Riplet in the antiviral response to HCV. Since Riplet is known to be inhibited by other RNA viruses, such as such influenza A virus, this innate immune signaling pathway may also be important in controlling other RNA virus infections.

Grazoprevir/elbasvir fixed-dose combination for hepatitis C.

Hepatitis C virus (HCV) infection is an increasing public health concern with an estimated 184 million people infected worldwide and approximately 350,000 deaths yearly from HCV-related complications. There is a compelling medical need for new anti-HCV therapeutic agents that are potent, tolerable, safe, completely oral and with shorter treatment duration. To this end, a plethora of direct-acting antivirals have been developed and regulatory authorities have approved nine new molecules for the treatment of chronic hepatitis C (CHC). In January 2016, the U.S. Food and Drug Administration approved the fixed-dose combination medication incorporating the NS3/NS4A inhibitor grazoprevir (formerly MK-5172) and the NS5A inhibitor elbasvir (formerly MK-8742), with or without ribavirin, for the treatment of CHC genotypes 1 and 4 infection in adult patients. This all-oral combination has proven potent and safe even in patients with advanced kidney disease. Herein, we review the pharmacokinetics, clinical efficacy and safety profile pertaining to grazoprevir/elbasvir fixed-dose combination for CHC.

Faldaprevir for the treatment of hepatitis C.

Enormous progress has been made in the understanding of the hepatitis C virus and the development of novel therapeutic agents since the identification of the virus, from initial interferon monotherapy to PEGylated interferon in combination with ribavirin for 48-72 weeks that used to be the standard of care in hepatitis C virus therapy. However, this combination has limited efficacy and a significant side effect profile including flu-like symptoms, anemia, leukopenia, autoimmune disorders and depression, so it is often poorly tolerated. Recently, direct-acting antiviral agents, such as the first-generation NS3/4A protease inhibitors, have been added to this combination, improving the percentage of successful treatments. Faldaprevir is a first-generation, second wave, protease inhibitor that, when combined with PEGylated interferon and ribavirin, has been shown to increase treatment success with shorter treatment duration. Various direct-acting antiviral agent combinations in interferon-free regimens have been effective in over 95% of patients and are now in licensed use.